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- PDB-4apd: Liraglutide -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 4apd
TitleLiraglutide
ComponentsLIRAGLUTIDE
KeywordsHORMONE / GLUCAGON / GLUCAGON LIKE PEPTIDE-1 ANALOG
Function / homology
Function and homology information


glucagon receptor binding / negative regulation of execution phase of apoptosis / feeding behavior / positive regulation of calcium ion import / positive regulation of insulin secretion involved in cellular response to glucose stimulus / Synthesis, secretion, and deacylation of Ghrelin / positive regulation of gluconeogenesis / cellular response to glucagon stimulus / protein kinase A signaling / regulation of insulin secretion ...glucagon receptor binding / negative regulation of execution phase of apoptosis / feeding behavior / positive regulation of calcium ion import / positive regulation of insulin secretion involved in cellular response to glucose stimulus / Synthesis, secretion, and deacylation of Ghrelin / positive regulation of gluconeogenesis / cellular response to glucagon stimulus / protein kinase A signaling / regulation of insulin secretion / positive regulation of peptidyl-threonine phosphorylation / response to activity / gluconeogenesis / adenylate cyclase-activating G protein-coupled receptor signaling pathway / hormone activity / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / Glucagon signaling in metabolic regulation / Synthesis, secretion, and inactivation of Glucagon-like Peptide-1 (GLP-1) / Glucagon-type ligand receptors / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / positive regulation of peptidyl-serine phosphorylation / glucose homeostasis / G alpha (s) signalling events / G alpha (q) signalling events / secretory granule lumen / positive regulation of ERK1 and ERK2 cascade / receptor ligand activity / G protein-coupled receptor signaling pathway / endoplasmic reticulum lumen / signaling receptor binding / negative regulation of apoptotic process / extracellular space / extracellular region / identical protein binding / plasma membrane
Similarity search - Function
Glucagon / Glucagon/GIP/secretin/VIP / Peptide hormone / Glucagon / GIP / secretin / VIP family signature. / Glucagon like hormones
Similarity search - Domain/homology
N-hexadecanoyl-L-glutamic acid / Pro-glucagon
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodSOLUTION NMR
AuthorsLudvigsen, S. / Steensgaard, D.B. / Thomsen, J.K. / Strauss, H. / Normann, M.
CitationJournal: To be Published
Title: Liraglutide
Authors: Steensgaard, D.B. / Thomsen, J.K. / Strauss, H. / Normann, M. / Ludvigsen, S.
History
DepositionApr 2, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 10, 2013Provider: repository / Type: Initial release
Revision 1.1Jan 29, 2014Group: Database references / Source and taxonomy / Structure summary
Revision 2.0Jun 14, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Other
Category: atom_site / database_2 ...atom_site / database_2 / pdbx_database_status / pdbx_nmr_software / struct_conn / struct_site
Item: _atom_site.Cartn_x / _atom_site.Cartn_y ..._atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_cs / _pdbx_database_status.status_code_mr / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 2.1Nov 6, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _pdbx_entry_details.has_protein_modification
Remark 650 HELIX DETERMINATION METHOD: AUTHOR PROVIDED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: LIRAGLUTIDE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,7732
Polymers3,3881
Non-polymers3861
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 20LEAST RESTRAINT VIOLATION
RepresentativeModel #1

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Components

#1: Protein/peptide LIRAGLUTIDE / GLUCAGON-LIKE PEPTIDE 1(7-37)


Mass: 3387.713 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: LIRAGLUTIDE IS A HUMAN GLP-1 ANALOG / Source: (gene. exp.) HOMO SAPIENS (human) / Production host: SACCHAROMYCES CEREVISIAE (brewer's yeast) / References: UniProt: P01275
#2: Chemical ChemComp-D6M / N-hexadecanoyl-L-glutamic acid


Mass: 385.538 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H39NO5
Has protein modificationY
Nonpolymer detailsLYS(GAMMA-GLU-PALMITOYL) (D6M): POSITION 26 IS LYSINE-GAMMA-GLU-PALMITOYL
Sequence detailsIN POSITION 26 LYSINE IS MODIFIED WITH LYS(GAMMA-GLU- PALMITOYL)

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111NOESY
121TOCSY
NMR detailsText: TOCSY AND NOESY DATA FOR ASSIGMENT AND MODEL BUILDING. STRUCTURE IS COMPOSED OF 2 HELICES WHICH ARE POORLY ORIENTED RELATIVE TO EACH OTHER

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Sample preparation

DetailsContents: 10% D2O / 90% H2O
Sample conditionspH: 7.9 / Pressure: 1.0 atm / Temperature: 300.0 K

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NMR measurement

NMR spectrometerType: Bruker AMX / Manufacturer: Bruker / Model: AMX / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
XPLOR 3.1, CNXCNXBRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU,READ, RICE,SIMONSON,WARRENrefinement
Prontostructure solution
X-PLORstructure solution
CNXstructure solution
NMR ensembleConformer selection criteria: LEAST RESTRAINT VIOLATION / Conformers calculated total number: 20 / Conformers submitted total number: 20

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